OUTPUT_DIR=../../output


# Ch. 21 & 1
#DATA_DIR=/home/luo_group/data/snp_data/human
#time ./gsnp -i $DATA_DIR/human18_sort/human18-chr21 -d $DATA_DIR/hg18_ref/chr21.fa -o $OUTPUT_DIR/chr21.cns -M $OUTPUT_DIR/chr21.mat -u -t -L 100 -s $DATA_DIR/dbSNP/dbSNP.chr21.sort -2 -C


# Ch. 1
DATA_DIR=/home/luo_group/data/snp_data/human
time ./gallop -i /lhome/mian/project/output/chr21.soap.sort -d $DATA_DIR/hg18_ref/chr21.fa -o $OUTPUT_DIR/chr21.cns -M $OUTPUT_DIR/chr21.mat -u -t -L 100 -s $DATA_DIR/dbSNP/dbSNP.chr21.sort -2 -C

